The Folly of Man
by bucketbot
Summary: There were no bijū or jinchūriki; there was only man and his mistakes.


**Welcome to my story, The Folly of Man.**

**I do not own Naruto. This applies to all future chapters as well. **

**Edit 05/10/2013: I greatly edited and expanded this prologue so it would be prudent to read it again. You don't have to, as the core concept and plot points haven't changed, but nonetheless a lot has been added.**

* * *

The Elemental Nations were a strange and curious place. It was a land where those of the shadows had taken to the light. Shinobi, the supposed masters of stealth and deception, destroyed large swathes of land and met openly in the field of battle. War was an inevitability and shinobi were only too happy to throw themselves at death. They were the pawns of this era and to that end great villages had been constructed where new generations of soldiers were to be trained.

Of these many villages, there were five whose military prowess was so great that they were called the Great Five. Each of these villages was well known for a particular attribute. The village said to be the greatest of the five was Konohagakure no Sato.

Konohagakure no Sato was known to most of the world as a village of idealists and lovers of peace. In the deadly world they inhabited, many saw them as foolish children preaching naive ideals. Heedless of how others perceived them, they stood as a shining beacon of morality in a lawless world. Their slogan of teamwork and perseverance was regarded as one of their greatest strengths. Unfortunately, all of it was a carefully crafted façade, one could see through it simply by looking hard enough.

The same debauchery played itself out night after night on the shadier streets of the village. There were those who lacked the power to protect themselves and simply vanished never to be heard of again. The feeble and poor wandered the streets, wishing for something more and hoping to make it through to another day. An army of shinobi, either hidden or in plain sight, wandered throughout the streets. Even they were not free from the shackles of greed and it was not uncommon to see a blind eye turned to the worst of crimes. It was the same as every other shinobi village. The streets were not safe.

The same political and economic power struggles existed in Konoha as they did everywhere else. Those with money and influence used their power to elevate themselves above and at the expense of all others. Many a child would see a day without food while an extravagant feast was thrown elsewhere for little to no reason. A woman fool enough to refuse a noble's company could soon find herself without a choice. Of course it was not only the weak who were preyed upon, any competitors who dropped their guard were swiftly eliminated through means legal or otherwise.

Outside of the village, the shinobi of Konoha did not hesitate to murder those that presented themselves as obstacles to a mission. Some did not hesitate to use their strength to take what they wanted. However, their comportment during a mission was only one side of the story. Some of the missions that the village took were missions of death and destruction. Entire families and smaller villages owed their non-existence to the loving shinobi of Konoha.

The worst of all was what no one looking in from the outside could see. The darkest secrets of the village were known only to those few of significant power. Of all the many secrets, there was one so terrible that even the implication of its existence was punishable by death. For deep within the bowels of the city was a hidden laboratory, within which any ideas of morality or human decency were discarded at the door.

* * *

_Konoha 15 years ago_

Four elderly people gazed down upon a new born baby. Lit by the moonlight, they could barely see the child as it slept, completely unaware of what was happening. The four watchers were careful as they moved towards the baby, unwilling to step in the pools of blood that were near omnipresent.

One of the watchers neared the child reached out carefully towards it, almost hesitant to touch it. Picking the child up with his only good arm, the other was bandaged, the man turned to another of the group. By the way that all three looked at him, it was clear that this other man, who radiated power, was their leader.

"Normally I would not be so hesitant to do this, but the fact that you aren't is what stops me. Are you sure we should be doing this? Once we go down this road, there will be no coming back." The bandaged man was not one to normally shy away from any unsavoury activities, but what was being considered made even him uneasy.

"The child's parents were heroes in life and so too will the child be. Do not forget, we are not the first who will have done this. Quite the opposite in fact." The leader spoke in a clear and unwavering voice, hoping to convey the utmost confidence. Another of the group, a female, decided to voice what everyone, including the leader, was thinking.

"We might not be the first, but we will be the worst. This goes against so many things our village claims to believe in. Are we truly ready to do this and live with the repercussions?" The group fell silent, each contemplating exactly what they were intending to do. The leader, a look of resignation on his face, spoke up.

"We do what we must to protect Konoha."

* * *

"Atsushi-san, do you have any idea why you have been called here today?" A middle aged man with unkept brown hair had a look of anxious curiosity on his face. He stood before the most powerful man in his village, the man who held the title of Hokage, Hiruzen Sarutobi. Whatever he had been brought before the man to discuss was clearly serious. Although his leader was an older man, noticeable through his greying hair and goatee, he never really seemed as old as he truly was. Tonight was different as the great shinobi seemed almost every day his actual age.

"I'm afraid I do not Hokage-sama." Astsushi's eyes were drawn to a small bundle that his leader was holding within his arms.

"Our village has suffered an unimaginable loss this past week. Although sorrow still weighs heavily in all our hearts, we cannot lose sight of the future." Sarutobi paused, both to gather his thoughts and to calm himself.

To Atsushi it seemed as if his leader had rehearsed everything before hand. Although a great leader, Sarubobi was not one to write his speeches unless the issue was of the utmost importance. Whatever was going on clearly had something to do with the bundle in his hands and Atsushi was getting worried.

"Our loss is one that other's see as their gain. Worse still, humans are greedy by nature and will not stop until they have gained all they can. We must be prepared for such an eventuality. It is for this reason that it has been decided that my former student's work shall be restarted. You will be the man in charge of this undertaking."

Atsushi felt all the colour leave his face. He knew exactly who and what his leader was referring to. What he was being asked to do was a terrible and unspeakable deed. The smartest of the Hokage's apprentices had been banished and declared as the most vile of creatures for attempting what Atsushi was being ordered to do. In the midst of his horror, Atsushi was only able to utter one word.

"Who?" Perhaps worst of all was that Atshushi already knew the answer. Lifting the bundle in his arms, Sarutobi showed Atsushi exactly what he feared. Wrapped in blankets was a tiny new-born child.

"Their child will be the one. Perhaps one day their spirits and Kami-sama herself will forgive us."

* * *

_Konoha 10 years ago_

Atsushi was sitting in a darkened room, watching Project Nine through a one-way mirror. The young child sat meditating in a room with an instructor carefully watching him. It was the day that the child was to unlock its chakra. This was a pivotal moment in the project, as it would be when they could truly begin to verify if their initial experiments had succeeded.

The child was meant to be a super soldier who could counter those that other villages had. The child would be trained constantly and be indoctrinated to love the village above everything else. The perfect chained dog, ready to defend its masters from any threat. That was one of the reasons this was an important step.

There was more to it than just that though. With the proper training, the child's chakra stores would be monstrous which would greatly aid them. The child had a natural healing ability that was almost unnoticeable. It was theorized that the regenerative abilities were actually dependent on his chakra, not something that was simply innate. If they turned out to be correct, the child would be capable of withstanding some incredibly invasive tests.

Tests wouldn't be the only thing the child would go through. Full body enhancements could be done to him even when he was older. Normally only a very young child had the required malleability to undergo the procedures, but with a natural healing ability, the age could moved up to perhaps even the teenage years.

It would be likely that the child would never leave the laboratory. Plans to make him a super soldier would be secondary. It was doubtless that Atsushi and his lab would be ordered to find a way to gift others with the child's regenerative abilities. An army who could heal themselves was something too great to pass up. They would not be allowed to stop until they discovered the secrets of the child's healing.

Just thinking about what he was going to be ordering made Atsushi shiver in disgust. Already he had done and commanded terrible deeds, but they would pale in comparison to what was coming.

Turning his focus back to the child, he noticed with some measure of sadness that the child had already completed the task. Nodding to an assistant, he had the order be put through to test the child.

Watching as one man held the poor kid down while another cut him, Atsushi nearly vomited. He fervently hoped that what he was doing was worth it. Such a little child should never have to be submitted to such things. They should be out playing and having fun, learning about the world around them. That he should be a part of stealing away the innocence of one so young made him consider leaving the project and the village.

Despite that, he knew he wouldn't. He knew far too many secrets and he wouldn't get more than a hundred feet outside of the village walls before a kunai would find its place in his back. So he sat and watched in muted horror as the cut began to heal.

* * *

_Konoha 5 years ago_

Watching as the subject once more healed from the wounds inflicted upon him, Atsushi couldn't help but marvel at the regenerative abilities that it possessed. The child was capable of healing any damage done given enough time. Death was still completely possible, but it would be unlikely that the subject would ever die from being wounded. It could even go so far as real regeneration of digits.

That had been a terrible day. Even now Atsushi would dream of the day where he took the subject and cut one of its fingers off. Even now he could recall the brutality of the act. It had been deemed necessary for the subject to be awake, as when asleep its abilities were not fully active. The child's screams hadn't made it any better. Truthfully though, he felt it was worth it to watch a new finger slowly grow back over the course of a week. Besides, he had far worse memories than that.

He was right when he thought that Project Nine would become a laboratory specimen due to its healing. The moment that the Hokage heard of it, he ordered that all efforts be focused on replicating the ability.

The project's initial aims had already been achieved, the subject was enhanced and more than ready to be sent out into the field. It was only through his own passionate defence of the idea that the Hokage agreed to let him keep the subject and continue his research.

There were so many tests and experiments that could be done that to simply shove the subject out to fight as a pawn was useless. Although the main goal was eluding them, they had managed to greatly improve the village. Having such a powerful ability, the subject was ideal for testing new medical advances. Already they had managed to cut down the number of deaths in seriously injured patients.

With the subject's abilities, intensive studies had been done to understand it's limits and provide the perfect training regimen. In fact, the village now used a watered-down version of the subject's training for those in the academy. Many more things had been discovered through the subject and the village was prospering from them.

For all that had been gained, Atsushi was glad to have been a part of the process. The village and so many people were benefiting from it that he felt it was worth all the pain. It really was for the greater good. With that in mind he made his way over to the subject to begin the next round of testing.

* * *

_Konoha Present Time_

"What do the results of the recent tests indicate?" Two men wearing lab coats were walking together down a dimly lit corridor. Both were moving rather quickly and had an anxious air about them.

"Unfortunately, we are still no closer to understanding how to replicate the subject's regenerative abilities. The most we've been capable of achieving is improving the rate of regeneration. Here is the full report Atsushi-san." Receiving the file from his subordinate, Atsushi began to read through the relevant parts. Slowing down, Atsushi flipped a page and frowned.

"Hmm, this is problematic. Ever since we finished Project Nine, we've been unable to come up with any more beneficial findings. Fumio-san, if we are incapable of producing something of use, the subject will be taken away prematurely. The higher ups finally wish to make use of his abilities. If it was up to me, the subject would never leave this building, but orders are orders. We either make progress or the subject is no longer ours." He slowed down to a complete stop and tightened his grip on the folder, trying to refrain from showing his anger in front of his subordinate.

Noticing Atsushi's mood, Fumio decided to suggest something that was slightly unorthodox. "It is my opinion that we cease to focus on this problem and begin other tests. With the subject's ability to heal itself, we should be able to conduct far more invasive tests far more often. We could potentially discover a far more efficient method of human augmentation. We have gained many valuable insights from the subject and this might be enough to convince them to leave it to us."

Atsushi glanced at Fumio in thought. "Perhaps. Do you have the recent reports from the trainers? I would like to review the subject's physical capabilities."

"Right away sir." The aide rushed into a room not far away. He soon reappeared with a folder in his hands. Taking the folder from his aide, Atsushi quickly began to scan the contents. It was the same as always and merely served to confirm his thoughts.

"This report conforms with the results of all the previous ones. The subject seems to not only have improved base capabilities, but the ability for growth has also been increased. If we could replicate these results on a much larger scale then it is doubtless that Konoha would become an unstoppable force. However, such augmentations are only capable due to the regenerative abilities that the subject originally possessed before Project Nine began. It all comes back to the same problem. We need to replicate the subject's ability or else we are most likely wasting our time." It was easy to say, but they had been failing for the better part of two years to discover the secrets of the subject's ability.

Fumio's brow furrowed in thought. "I know we have discussed this before, but what about Orochimaru? Is our research not based off his earlier attempts at this very project? I had heard rumours of him bypassing the need for regenerative abilities." At one point the entirety of Konoha's scientific breakthroughs could be attributed to a single man. Orochimaru headed numerous projects within the village before being declared a traitor and fleeing the village.

"That may or may not be true, but it is irrelevant. Whatever breakthroughs Orochimaru might have made into that area are inaccessible to us as we lost most of his data. The majority of Project Nine was built from scratch, very little actually came from that man's research. The only thing we might garner from any of this is that it _might _be possible to augment humans without the need for them to be like Project Nine. Even if it were true, we simply don't have enough time to start a whole new line of tests. Any of our former forays into that area of study have been met with failure." Fumio frowned; he too did not wish to lose the ability to study such a magnificent specimen.

"What else can we do then?" Atsushi seemed lost in thought for a while before he answered.

"For now just run another set of the standard tests, I need to think." Atsushi was already walking away before Fumio even had the chance to reply. Somewhat annoyed by the dismissal, Fumio made his way over to the area where they kept Project Nine.

Even as he walked over to perform what he saw as another round of useless tests, he couldn't prevent his mind from contemplating how exactly they could solve the problem that faced them. Perhaps he could run a few extra tests on the subject; after all, it wasn't as if it could hurt. However, when he got to the room, he stepped on something sticky. Looking down, he saw blood. In a panic he pushed the door open only to lose all colour in his face.

"Oh shit." Shattered equipment and broken bodies lay everywhere, but the test subject was nowhere to be found.

* * *

"Hokage-sama!" Fumio stood, out of breath, in the office of the Hokage. After reporting the disappearance to Atsushi, Fumio had run the entire way to deliver the bad news.

"I hope what you have to say is important." Normally Sarutobi would have already had the man thrown out of his office, but the very fact that he dared burst in looking so disheveled was of interest. This was twofold as Sarutobi recognized the man as one the leading scientists from the hidden research division. Anything that could bring the man to look so anxious was almost assuredly a matter of great importance.

"I beg your pardon Hokage-sama, but I bring terrible news. Project Nine has escaped!" Looking at his leader now, the scientist couldn't help but be terrified. Very few things made the man serious, let alone angry as he was now. Muttering a small prayer for his life, Fumio awaited his leader's reaction.

"You mean to tell me that what amounts to the future of our village has escaped? The one thing that we threw away everything we stand for to achieve has escaped?" The deadly calm with which Sarutobi spoke only terrified the scientist even further. He'd be lucky to still be alive by the end of this conversation.

"Y-yes Hokage-sama." Doing his best to keep some measure of dignity before his death, he held his head up high and managed to keep the quiver in his voice to a minimum.

"Anbu, gather our best tracking teams that are on hand. I want this dealt with promptly. Failure is not an option." Out of the shadows of the room, two masked individuals stepped forth, bowing.

"It will be done Hokage-sama." Both ninja quickly disappeared from sight, leaving an anxious man staring at Sarutobi.

"What about me Hokage-sama?" Although he was still worried about his fate, he had to ask. Better to see his death coming than to have a knife slipped between his ribs as he left. Sarutobi regarded him with serious eyes for a few moments before responding.

"Begin project ten." The scientist's eyes widened, he was unable to believe what he had just been told. Project ten was not something that any of them had thought would be allowed to proceed, as it was perhaps even more controversial than the previous project.

"Project ten Hokage-sama? Are you sure?" Sarutobi nodded gravely. This was not something that he had wished to condone, but the circumstances forced him to this decision.

"I did not misspeak nor did I speak without thinking. We have already done many terrible things and this is simply one more. We need an ace should Project Nine not be retrieved. Go and do as I have commanded." Bowing, the scientist left, unsure if what he had been asked to do was worse than being killed or not.

* * *

"I request to be a part of the search team." A man with spiky silver hair now stood in front of the Hokage. Although most of his face was covered by a mask and one of his eyes hidden, it was easy to see the serious expression with which the man spoke.

"Do you believe that to be wise Kakashi-san? After all, this is something that you have some personal stake in." Sarutobi stared at his subordinate sharply. This man had a connection to Project Nine that none knew about. It was only a courtesy that Kakashi had even known of the existence of Project Nine, as he would have normally not had the authorization to gain any knowledge on it.

"It's for exactly that reason that I have to go Hokage-sama. I owe a great debt and I've so far failed to repay it. Please allow me this chance at making amends." It was unusual to hear the man speak so passionately about anything. It was not something that convinced Sarutobi, it merely made him doubt the man further.

"You are not one who usually let's their emotions rule them so easily when it comes to your missions." Kakashi knew that was the truth, but he couldn't help himself. This was not an issue that he could ignore or approach half-heartedly.

"Of course they rule me now. You know exactly why as well." Sarutobi shook his head, weary of the discussion already. He knew full well exactly how important this mission was to the man in front of him. He could not allow one man's need to redeem himself to jeopardize a mission of such great importance, even if Sarutobi understood his feelings perfectly.

"It is for that that I hesitate. Clearly you are not yourself and such a mission needs one hundred percent focus. Can you honestly tell me that you would be capable of completing this mission as if it were any other?" Kakashi couldn't believe what he was hearing. Wasn't plain to see that he would rather die than fail this particular mission? How could the Hokage have such a lack of faith in one of his most talented subordinates?

"It's too important to me, there's no way I would jeopardize it." Sarutobi couldn't help but noticed the sincerity in every word. Kakashi truly believed that he would be capable of aiding the mission in his current state. Unfortunately, belief in yourself meant nothing if it was misguided.

"I'm sorry, but I deny your request and forbid you from taking part in the mission in any way. Dismissed." He did indeed sound genuinely sorry, but it did little to improve Kakashi's mood.

It was with a heavy heart that Kakashi left the office. He hadn't expected to be rejected and he was now unsure of what to do. He had to go, there was no question, but he had been commanded to keep himself away from the retrieval team. What was a loyal shinobi to do? He couldn't exactly disobey his leader, but he couldn't stand on the sides. He had to choose one over the other and there was no easy answer to his problem.

He wandered the streets of the village, lost in thought. Eventually his feet brought him along a path that he knew all to well. He had ended up standing in front of the memorial stone that had the names of all who died in action written on it. He stared at the list of names, easily finding the familiar ones. He stopped at two specific names that were written one after another.

It was still easy for him to remember the faces of the two. In his life Kakashi had met very few people he liked and even less that he loved. The two whose names were written had been of that select few he loved. They had been almost as parents to him and yet he had turned his back on their only child.

_'What should I do?'_ The debt that he owed was a great one. Additionally, it was not just honour that pushed him to disobey; it was a genuine wish to help. He couldn't ignore the need to help, he had already failed so many other people that he cared for.

_'For me to idly stand by while such depraved acts were committed, how can I justify any further inaction? Not even Hokage-sama will stop me from doing what needs to be done._ _I'm sorry that it ended up like this sensei. Perhaps it's a blessing that you aren't alive to see what has become of your son.'_

* * *

A figure in a brown cloak was racing through a forest near Konoha at great speeds. It was clear that the intent was to run away from the village without care for where they headed. Unfortunately, that lack of care extended to covering their tracks. A clear path of broken branches and footprints lead all the way back to the village; a trail so clear that even a newly graduated shinobi would be capable of following. During its mad rush, the hood of the cloak caught on a branch and was pulled off the figures head, revealing blonde hair, piercing blue eyes, and three whisker marks on each cheek.

* * *

**That's it for now. This is my third story and I hope it wasn't a terrible start. Quite frankly, I was unsatisfied with the first version of this prologue as it didn't quite fit the idea I had for this story. ****Hopefully my massive re-haul of this prologue has been a major improvement. I hoped to add a bit more in terms of back story and at the same time make it simply more in depth than the original. That and I actually came across a story with an author's note that was longer than the original chapter, which really bothered me.**

**As you might be able to tell, this story will be a rather long tale that is utterly different from cannon. I'm also hoping that it will be significantly different from most other Naruto stories. I really wanted to try something new and, while they might be out there, I've never read a story with this idea. Hopefully there isn't some super awesome story like this out there that I'll try and fail to live up to.**

**********If you haven't read my other two stories, The Path to Peace and The Twins, then you totally should. Speaking of that, I feel as if my writing has noticeably improved from the first chapter of PTP to this prologue. Hopefully it has, else I'm terribly biased.**


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